forcefield

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Purpose

The forcefield command is used to select a particular forcefield from the current forcefield file, to control calculations involving incomplete parameter sets, and to change and scale the contributions from various energy terms used in Discover calculations. The parameters modified by this command are in effect for all subsequent energy calculations, until modified by another forcefield command.

Syntax

forcefield ?path? ?keyword = value?...

Click to jump to the desired forcefield-control parameters:

How to handle missing parameters
Nonbond parameters
van der Waals parameters
Coulomb parameters
Parameters to scale the energy terms

Path/Keyword Values Default Meaning

select string $FORCEFIELD Name of forcefield contained in forcefield file.

How to handle missing parameters:

Jump to top of page param*eters Pathname to forcefield-selection parameters. bond_auto*matic Boolean true Use automatic bond parameters if no explicit ones are found. angle_auto*matic Boolean true Use automatic angle parameters if no explicit ones are found. torsion_auto*matic Boolean true Use automatic torsion parameters if no explicit ones are found. oop_auto*matic Boolean true Use automatic out-of-plane parameters if no explicit ones are found. bond_stop Boolean true End calculation with error if no parameters are found for some bond. If bond_automatic is also true, end only if no explicit or automatic parameters exist. angle_stop Boolean true End calculation with error if no parameters are found for some angle. If angle_automatic is also true, end only if no explicit or automatic parameters exist. torsion_stop Boolean true End calculation with error if no parameters are found for some torsion. If torsion_automatic is also true, end only if no explicit or automatic parameters exist. oop_stop Boolean true End calculation with error if no parameters are found for some out-of-plane. If oop_automatic is also true, end only if no explicit or automatic parameters exist. cross_stop Boolean false End calculation with error if no parameters are found for some cross term. If current forcefield has no cross terms this flag has no effect; it applies only when the forcefield has cross terms but lacks parameters for some cross term. print_auto*matic Boolean true List automatic and unfound parameters in the file run_name.prm.

Nonbond parameters:

Jump to top of page nonbond Pathname to nonbond parameters. separate_c*oulomb_cutoffs Normally, both van der Waals and Boolean false Coulombic interactions are calculated with same nonbond list. If this flag = true, 2 lists are used: 1 for van der Waals and 1 for Coulombic interactions.

van der Waals parameters:

Jump to top of page vdw Pathname to van der Waals parameters. summa*tion_method group*_based group_based Method by which energy terms atom*_based are summed in the calculation ewald when generating the nonbond cell_m*ultipole list. (Note on cell cell_b*ased multipole method.) no_cutoff cutoff real 9.5 Distance (angstroms) at which to exclude interactions from the nonbond list for atom_based and group_based methods (used only if no_cutoff is not used). spline*_width real 1.0 Size (angstroms) of region within which nonbond interactions are splined from their full value to zero for atom_based and group_based methods (used only if no_cutoff is not used). buffer*_width real 0.5 Distance (angstroms) beyond cutoff at which nonbond interactions are zero (but the atoms are included in the nonbond list) for atom_based and group_based methods (used only if no_cutoff is not used). update*_width real 1.0 Distance (angstroms) an atom may move before nonbond list is regenerated, for ewald, cell_multipole, and cell_based methods (always applies to both van der Waals and Coulomb nonbond lists). (Important note) cmm_level second second Highest-order multipole and third highest-order Taylor series fourth expansion coefficient used in cell multipole nonbond calculation. number_of_cells integer 1 Number of layers of cells to include in nonbond list, counting from the base cell, for cell_multipole and cell_based summation methods (e.g., 1 means all the cells one unit cell away-- the 26 immediate neighbor cells). ewald_acc*uracy real 0.0025 Accuracy (kcal mol^-1) used in Ewald calculations. (Note.) ewald_di*pole Boolean false If true, then contributions from dipole moment are taken into account in Ewald calculations. use_quartic Boolean false If true, then the quartic potential formula is used for the repulsive part of the nonbond interaction, the dispersive and coulombic parts are turned off, and the atom_based summation method is automatically used. quartic_radius_scale real 1.0 Scales the van de Waals radius for each nonbond interaction pair so that the interaction is ignored if the distance between the two atoms is larger than the scaled van de Waals radius for the pair. This is meaningful only when use_quartic is true.

Coulomb parameters:

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coulomb Pathname to Coulomb parameters. summa*tion_method group*_based group_based Method by which energy terms are atom*_based summed in the calculation when ewald generating the nonbond list. cell_m*ultiple (Note on cell multipole method.) cell_b*ased no_cutoff cutoff real 9.5 Distance (angstroms) at which to exclude interactions from the nonbond list for atom_based and group_based methods (used only if no_cutoff is not used). spline*_width real 1.0 Size (angstroms) of region within which nonbond interactions are splined from their full value to zero for atom_based and group_based methods (used only if no_cutoff is not used). buffer*_width real 0.5 Distance (angstroms) beyond cutoff at which nonbond interactions are zero (but the atoms are included in the nonbond list) for atom_based and group_based methods (used only if no_cutoff is not used). update*_width real 1.0 Distance (angstroms) an atom may move before nonbond list is regenerated, for ewald, cell_multipole, and cell_based methods (always applies to both van der Waals and Coulomb nonbond lists). (Important note) cmm_level second second Highest-order multipole and third highest-order Taylor series fourth expansion coefficient used in cell multipole nonbond calculation. number_of_cells integer 1 Number of layers of cells to include in nonbond list, counting from the base cell, for cell_multipole and cell_based summation methods (e.g., 1 means all the cells one unit cell away-- the 26 immediate neighbor cells). ewald_acc*uracy real 0.0025 Accuracy (kcal mol^-1) used in Ewald calculations. ewald_di*pole Boolean false If true, then contributions from dipole moment are taken into account in Ewald calculations. distance_dep*endent_dielectric Boolean false Whether to use constant or distance-dependent dielectric for calculating Coulombic interactions. dielect*ric_value real 1.0 Magnitude of dielectric constant relative to ₀.

Parameters to scale the energy terms:

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scale Pathname to scale parameters. bond real 1.0 Scale the bond energy terms. angle real 1.0 Scale the angle energy terms. torsion real 1.0 Scale the torsion energy terms. oop real 1.0 Scale the out-of-plane energy terms. vdw real 1.0 Scale the van der Waals energy terms. coulomb real 1.0 Scale the Coulombic (charge) energy terms. cross real 1.0 Scale all the cross terms. hbond real 1.0 Scale hydrogen-bond energy terms. vdw_1_4 real 0.5 Scale the 1-4 van de Waals interactions for the Amber forcefield. No effect for other forcefields. coulomb_1_4 real 0.5 Scale the 1-4 Coulombic interactions for the Amber forcefield. No effect for other forcefields.

Description

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The forcefield command may be used to select one of the forcefields contained in a forcefield file. If this command is not specified, the default is to use the forcefield with the same name as the file. This command is currently available only with the CVFF forcefield file. This forcefield file contains the following forcefields:

cvff: default--cross terms and Morse bonds
cvff_nocross: Morse bonds but no cross terms
cvff_nomorse: cross terms but quadratic bonds
cvff_nocross_nomorse: no cross terms and quadratic bonds

In addition, the forcefield command is used to specify the Discover program's behavior for forcefields that contain automatic parameters. The default is to use automatic parameters for any interactions for which there are no explicit parameters. This can be disabled on a per-term basis. For instance, setting oop_automatic to false disables automatic parameter assignment for the out-of-plane interactions.

The _stop parameters are used to control whether the Discover program exits with an error when parameters are not found for any interaction. The default behavior is that the Discover program stops if any bond, angle, torsion, or out-of-plane term is not found but continues for unfound cross terms, just setting the parameters for any missing cross terms to zero.

The forcefield command is also used to control the methods used in calculating nonbond interactions. Some of the methods available for nonbonds are:

Calculate all the nonbond interactions in the system (summation method = no_cutoff).
Atom-based cutoffs--generate a list of nonbond interactions based on all the atoms within the (cutoff + buffer_width) distance from an atom.
Group-based cutoffs--generate a list of nonbond interactions based on the charge groups within the (cutoff + buffer_width) distance from a charge group. The advantage of this method over atom-based cutoffs is that dipoles are not broken at the cutoff (since charge groups are neutral), but it does require the specification of the charge groups.
Use the Ewald, cell-multipole, or cell-based methods.

It is possible to have two different lists--one for van der Waals interactions (vdw) and one for electrostatic interactions (coulomb). This allows, for instance, use of a large cutoff for electrostatics and a smaller cutoff for van der Waals (since these interactions fall off more rapidly).

The lists are automatically updated whenever any atom moves more than buffer_width/2. This prevents any discontinuities from arising due to atoms moving from outside the nonbond list directly into the spline region.

The forcefield scale command offers control over the individual types of energy terms in the forcefield.

Note that the forcefield command differs from other BTCL commands in that the parameter values specified are retained, i.e., the parameter default values are set when the command is performed. For example:

cdlConfig forcefield select = cvff_nocross parameters
	bond_automatic = FALSE  scale angle = 1.1

forcefield scale bond = 1.1

would be identical in functionality and operation to:

forcefield select = cvff_nocross parameters
	bond_automatic = FALSE  scale angle = 1.1

forcefield scale bond = 1.1

Whether to scale 1-4 interactions is determined by the keyword amber in the name of the forcefield file--if the word amber is not part of the name of the forcefield used, 1-4 scaling is not done. 1-4 van der Waals and 1-4 Coulombic interactions are scaled separately (as required by the new AMBER forcefield). The default scale factors are 0.5 for both. These two scale factors (vdw_1_4 and coulomb_1_4) just like any other scale factors. However, they have no effect on the energies if amber is not part of the name of the forcefield used.

Note on update_width keyword: For the Ewald and cell multipole methods, the update frequency of neighbor lists or Taylor coefficients is determined by update_width. If update_width is small (e.g. 0.0000001 Å), the neighbor lists or Taylor coefficients may be updated at every energy evaluation. By default (update_width = 1.0 Å), the neighbor lists or Taylor coefficients are updated whenever an atom moves more than update_width from its original position. Thus, the number of steps of dynamics or minimization that occur between updates increases. In minimization runs, an energy discontinuity may result. This is because the neighbor lists or Taylor coefficients are created at one geometry and used for energy evaluations at that geometry as well as the slightly different geometries of subsequent steps. The discontinuity becomes apparent if the final geometry is evaluated later (in a subsequent energy command), since new neighbor lists and Taylor coefficients are generated. An appropriate value of update_width depends on the application. More frequent updates of the Taylor coefficients slow down the cell multipole method, but make it more accurate. The discontinuity is insignificant for the Ewald method.

Note on Ewald accuracy: Although the default Ewald accuracy is acceptable for most single-point energy calculations, a tighter accuracy may be required for some minimization and dynamics runs, to insure acceptable gradient accuracy. In particular, using 0.00025 may be preferable if your minimization run fails to converge or your dynamics run misbehaves.

Note on cell multipole method: Currently, the cell multipole method does not calculate second derivatives. For nonperiodic systems with fewer than 200 atoms, the cell multipole method is switched to the no_cutoff method if second derivatives are requested.

Also note that the cell_multipole method does not calculate virials (cell derivatives). Thus, cell minimization and constant-pressure dynamics cannot be carried out using this nonbond method.

If use_quartic is set to true, the cutoff parameter is not used. The nonbond repulsive energy is calculated using the quartic potential formula and is included only when the distance between the pair of atoms is less than the scaled van de Waals radius. The nonbond dispersive and Coulombic parts are automatically turned off. Also the atom_based nonbond summation method is automatically used. The use_quartic keyword should be set to false explicitly if a normal calculation is desired after the use of the quartic potential.

The Buckingham (exponential-6) nonbond interaction potential is also supported. To use this potential form, a section containing the appropriate forcefield parameters should be inserted into the forcefield file, for example:

#nonbond(exp-6) cvff

> E = Aij * exp(-r/rho) - Cij/r^6

!Ver  Ref    I    J            A              rho              C
!---- ---   ---- -------    --------        ---------       --------
 1.0  14     LR    O2        6740.43800        0.34720        0.00000
 1.0  14     LS    OS        6740.43800        0.34720        0.00000

Example 1

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forcefield select = cvff_nocross

This example of the forcefield command selects the cvff_nocross forcefield from the current forcefield file. Use of this command causes the energy expression to be recreated with the new forcefield parameters the next time an energy evaluation is performed.

Example 2

forcefield parameters bond_automatic = FALSE \ 
 	 angle_automatic = FALSE   \
 	 torsion_automatic = FALSE \
 	 oop_automatic = FALSE

This example of the forcefield command disables all use of automatic parameters.

Example 3

forcefield nonbond vdw summation_method = atom_based

This example of the forcefield command specifies that subsequent calculations use the atom-based method to generate the nonbond summation list. All other forcefield parameters are set to their current defaults.

Example 4

forcefield scale angle = 1.5

This example of the forcefield command indicates that the contributions of the angle energy terms are to be multiplied by 1.5. All other forcefield parameters are set to their current defaults.

Example 5

forcefield nonbond +separate_coulomb_cutoffs \ 
 	 coulomb cutoff = 12 spline_width = 1.5 \ 
 	 buffer_width = 0.5

In this example, the defaults specify the use of separate nonbond lists for the van der Waals and Coulombic energy terms and set the Coulomb list cutoff to 12 Å, the Coulomb spline width to 1.5 Å, and the Coulomb buffer width to 0.5 Å. This corresponds to a spline region going from the full value at 10.0 Å down to zero at 11.5 Å (followed by a 0.5-Å buffer region before the cutoff at 12.0 Å).

Example 6

forcefield scale \
    vdw_1_4 = 0.4 \
    coulomb_1_4 = 0.4

This BTCL statement is used to scale both 1-4 van der Waals and 1-4 Coulombic interactions by a factor of 0.4 for the AMBER forcefield. The statement has no effect if the forcefield used is not AMBER.

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